After upgrading Windows 10 to the Creators Update, I had the same problem as the OP. Most Win-X menu entries didn't work. In addition, I found that right-clicking ANY program file shortcut and choosing "Run as Administrator" ALSO was broken, no matter how the shortcut was located (e.g. from the Start Menu directly, pressing WIN and typing, desktop shortcuts, etc.) Very annoying when you have to run an elevated command prompt or PowerShell to make a system change!
Through a process of elimination I tracked it down to the MC shell integration (JRShellExt.dll). Disabling this context menu handler with a tool called ShellExView fixed the problem. So then I re-enabled it, then toggled the option in MC's settings off, and back on again, and the shell integration now works WITHOUT interfering with my Win-X menu or "Run as Administrator".
I don't know if this is permanent, another Windows update might just break it again.
aimhere